Journal
EVOLUTIONARY ECOLOGY
Volume 34, Issue 3, Pages 339-359Publisher
SPRINGER
DOI: 10.1007/s10682-020-10039-z
Keywords
Mutations; Viruses; Fitness costs; CpG sites
Categories
Funding
- NSF [1655212]
- National Evolutionary Synthesis Center (NESCent), NSF [EF-0905606]
- NIH MARC [T34-GM008574]
- NIH MA/MS-PhD Bridge Grant [R25-GM048972]
- NIH RISE Grant [R25-GM059298]
- NSF STC CCC Grant [DBI 1548297]
- Genentech Foundation MS Dissertation Scholarship
- Genentech Foundation fellowship
- Student Enrichment Office
- Division Of Environmental Biology
- Direct For Biological Sciences [1655212] Funding Source: National Science Foundation
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Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.
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